def _handling_of_preprocessing_state(self, job_id, launch_config):
job_directory = self._proxied_manager.job_directory(job_id)
try:
yield
launch_kwds = {}
if launch_config.get("dependencies_description"):
dependencies_description = DependenciesDescription.from_dict(
launch_config["dependencies_description"])
launch_kwds[
"dependencies_description"] = dependencies_description
for kwd in ["submit_params", "setup_params", "env"]:
if kwd in launch_config:
launch_kwds[kwd] = launch_config[kwd]
self._proxied_manager.launch(job_id, launch_config["command_line"],
**launch_kwds)
with job_directory.lock("status"):
job_directory.store_metadata(JOB_FILE_PREPROCESSED, True)
self.active_jobs.activate_job(job_id)
except Exception as e:
with job_directory.lock("status"):
job_directory.store_metadata(JOB_FILE_PREPROCESSING_FAILED,
True)
job_directory.store_metadata("return_code", 1)
job_directory.write_file("stderr", str(e))
self.__state_change_callback(status.FAILED, job_id)
log.exception("Failed job preprocessing for job %s:", job_id)
def _handling_of_preprocessing_state(self, job_id, launch_config):
job_directory = self._proxied_manager.job_directory(job_id)
try:
yield
launch_kwds = {}
if launch_config.get("dependencies_description"):
dependencies_description = DependenciesDescription.from_dict(launch_config["dependencies_description"])
launch_kwds["dependencies_description"] = dependencies_description
for kwd in ["submit_params", "setup_params", "env"]:
if kwd in launch_config:
launch_kwds[kwd] = launch_config[kwd]
self._proxied_manager.launch(
job_id,
launch_config["command_line"],
**launch_kwds
)
with job_directory.lock("status"):
job_directory.store_metadata(JOB_FILE_PREPROCESSED, True)
self.active_jobs.activate_job(job_id)
except Exception as e:
with job_directory.lock("status"):
job_directory.store_metadata(JOB_FILE_PREPROCESSING_FAILED, True)
job_directory.store_metadata("return_code", 1)
job_directory.write_file("stderr", str(e))
self.__state_change_callback(status.FAILED, job_id)
log.exception("Failed job preprocessing for job %s:", job_id)
def __extra_job_description_kwargs(options):
dependencies_description = None
test_requirement = getattr(options, "test_requirement", False)
if test_requirement:
requirements = [TEST_REQUIREMENT]
dependencies_description = DependenciesDescription(requirements=requirements)
test_env = getattr(options, "test_env", False)
env = []
if test_env:
env.append(dict(name="TEST_ENV", value="TEST_ENV_VALUE"))
return dict(dependencies_description=dependencies_description, env=env)
def __extra_job_description_kwargs(options):
dependencies_description = None
test_requirement = getattr(options, "test_requirement", False)
if test_requirement:
requirements = [TEST_REQUIREMENT]
dependencies_description = DependenciesDescription(
requirements=requirements)
test_env = getattr(options, "test_env", False)
env = []
if test_env:
env.append(dict(name="TEST_ENV", value="TEST_ENV_VALUE"))
container = getattr(options, "container", None)
remote_pulsar_app_config = getattr(options, "remote_pulsar_app_config",
None)
return dict(dependencies_description=dependencies_description,
env=env,
container=container,
remote_pulsar_app_config=remote_pulsar_app_config)
def setUp(self):
super(TestStager, self).setUp()
from .test_utils import get_test_tool
self.tool = get_test_tool()
self.client = MockClient(self.temp_directory, self.tool)
inputs = self.__setup_inputs()
self.client_job_description = ClientJobDescription(
tool=self.tool,
command_line="run_test.exe",
config_files=[],
input_files=inputs,
client_outputs=ClientOutputs(
"/galaxy/database/working_directory/1", []),
working_directory="/galaxy/database/working_directory/1",
dependencies_description=DependenciesDescription(
requirements=[TEST_REQUIREMENT_1, TEST_REQUIREMENT_2]),
env=[TEST_ENV_1],
rewrite_paths=False,
)
self.job_config = dict(
working_directory="/lwr/staging/1/working",
outputs_directory="/lwr/staging/1/outputs",
system_properties=dict(separator="\\", ),
)
open(join(output1_extras_path, "extra"), "w").write("EXTRA_OUTPUT_CONTENTS")
version_output.write("1.0.1")
output4_index_path.write(index_path)
finally:
output.close()
config_input.close()
output2.close()
output3.close()
version_output.close()
output4_index_path.close()
"""
EXPECTED_OUTPUT = b"hello world output"
EXAMPLE_UNICODE_TEXT = u'єχαмρℓє συтρυт'
TEST_REQUIREMENT = ToolRequirement(name="dep1", version="1.1", type="package")
TEST_DEPENDENCIES = DependenciesDescription(requirements=[TEST_REQUIREMENT])
class MockTool(object):
def __init__(self, tool_dir):
self.id = "client_test"
self.version = "1.0"
self.tool_dir = tool_dir
def run(options):
waiter = None
try:
temp_directory = tempfile.mkdtemp()
temp_index_dir = os.path.join(temp_directory, "idx", "bwa")
